This invention relates to the crystallization and resolution of the three-dimensional structure of the human complement receptor type 2 (CR2) protein, and to methods of using such structure, particularly for structure-based drug design of regulatory compounds.
Complement receptor type 2 (CR2 or CD21) is a key interface between innate and adaptive immunity by serving as the receptor for complement component C3d, as well as for C3 and fragments of C3 that contain the C3d domain or a portion thereof, including but not limited to C3dg, iC3b and C3b (D. T. Fearon and R. H. Carter, Annu Rev Immunol 13, 127-49 (1995); D. T. Fearon, Semin Immunol 10, 355-61 (1998)). C3d and other CR2-binding C3 fragments that contain C3d or a portion thereof are covalently attached to foreign antigens (such as invading microorganisms) through the action of the classical, alternative or lectin complement pathways (S. K. A. Law and K. B. M. Reid, Complement,. D. Male, Ed., In Focus (Oxford, UK: IRL Press., ed. second edition, 1995)). C3d- or other CR2-binding C3 fragment-bound antigens then greatly amplify B cell responses by binding to CR2 through these C3 fragments at the same time as engaging the B cell receptor (BCR) via the bound antigen (R. H. Carter and D. T. Fearon, Science 256, 105-7 (1992); J. C. Cambier, Biochem Soc Trans 25, 441-5 (1997)). The cross-linking of CR2 to the BCR by C3d, C3, or other CR2-binding fragments of C3 that contain C3d or a portion thereof greatly amplifies a signal transduction cascade through the CR2/CD19/CD81 co-activation complex (D. T. Fearon, 1995 ibid.; D. T. Fearon, 1998, ibid.; J. C. Cambier, 1997, ibid.; A. K. Matsumoto, et al., J Exp Med 173, 55-64 (1991)).
Human CR2 is also the obligate receptor for the Epstein-Barr virus (EBV) through its interactions with the gp350/220 viral membrane protein (J. D. Fingeroth, et al., Proc Natl Acad Sci USA 81, 4510-4 (1984)). EBV causes infectious mononucleosis, and is associated with Burkitt""s Lymphoma and several other lymphomas and non-lymphoid tumors (M. Okano, Acta Paediatr 87, 11-8 (1998)). In addition, human CR2 serves as a receptor for CD23 (J. P. Aubry et al., Nature 358, 505-7 (1992)) and is thus a receptor for at least three biologically important ligands. Using genetically manipulated mice and animal models, CR2 has been shown to be essential for the development of normal humoral immunity to T-dependent antigens (T. Hebell et al., Science 254, 102-5 (1991); J. M. Ahearn, et al., Immunity 4, 251-62 (1996); H. Molina, et al., Proc Natl Acad Sci USA 93, 3357-61 (1996)) as well as possibly play an important role in the maintenance of B cell self-tolerance and the development of autoimmunity (A. P. Prodeus, et al., Immunity 9, 721-31 (1998)). CR2 has also been shown to mediate the interaction of C3-bound HIV-1 as an immune complex with B cells in a fashion that promotes transfer of virus and infection of CD4 T cells (S. Moir, et al., J Exp Med 192, 637-46 (2000)). CR2 also mediates direct infection of CR2-expressing T cells or other CR2-expressing cell lineages that are bound by HIV-1 immune complexes containing C3, C3d or other CR2-binding C3 fragments (including, but not limited to, HIV-1 complexed with C3d).
Interactions with all three human CR2 ligands require the first two of 15 or 16 short consensus repeat (SCR) domains (C. A. Lowell, et al., J Exp Med 170, 1931-46 (1989); J. C. Carel et al., J Biol Chem 265, 12293-9(1990)). SCR domains, like Ig domains, are found in many proteins from both complement and non-complement families, and mediate diverse biological functions (A. P. Wiles, et al., J Mol Biol 272, 253-65 (1997)). Several of the SCR proteins also serve as receptors for important human pathogens. For example, in addition to CR2, CD46 is a Measles Virus receptor (R. E. Dorig et al., Cell 75, 295-305 (1993)), and CD55 is an echovirus receptor (T. Ward, et al., EMBO J 13, 5070-4 (1994); J. M. Bergelson, et al., Proc Natl Acad Sci USA 91, 6245-9 (1994)). Previously determined structures of SCR proteins containing two or four SCR domains have revealed a conserved core structure but variable orientations between domains mediated in part by relatively short 3-8 amino acid inter-SCR linker peptides (A. P. Wiles, et al., 1997, ibid.; P. N. Barlow, et al., J Mol Biol 232, 268-84 (1993); J. M. Casasnovas et al., EMBO J 18, 2911-22 (1999); R. Schwarzenbacher, et al., EMBO J 18, 6228-39 (1999)). As one of the major functions of SCR domains is to mediate protein-protein (such as receptor-ligand) interactions, and at least two SCRs have been found to be required for these interactions, the relative angle and orientation unique to each SCR-containing protein is likely to contribute to both biologic diversity as well as specificity. However, the lack of a high-resolution structure of a receptor-ligand complex in this family has hindered the understanding of the molecular recognition mechanisms of this class of proteins. With regard to the structure of CR2 and the molecular interactions with its ligands, C3d and EBVgp350/220, variable results have been obtained using mutagenesis, monoclonal antibody, and peptide strategies (C. A. Lowell, et al.,J Exp Med 170, 1931-46 (1989); D. R. Martin et al., J Exp Med 174, 1299-311 (1991); H. Molina, et al., J Biol Chem266, 12173-9(1991); H. Molina et al., J Immunol 153, 789-95 (1994); D. R. Martin et al., J Virol 68, 4716-26 (1994); H. Molina, et al., J Immunol 154, 5426-35 (1995)). 
Therefore, there is a need in the art for a three dimensional structure of CR2 in order to better understand the molecular recognition mechanisms of the protein and to enable the identification and/or design of compounds that mimic, enhance, disrupt or compete with the interactions of CR2 with its ligands.
One embodiment of the present invention relates to a method of structure-based identification of compounds which potentially bind to complement receptor type 2 (CR2) proteins or to a complex of CR2 and its ligand. This method includes the steps of: (a) providing a three dimensional structure of a CR2 short consensus repeat (SCR) 1-2 region; and, (b) identifying a candidate compound for binding to the CR2 SCR 1-2 region by performing structure based drug design with the structure of (a). The three dimensional structure of a CR2 short consensus repeat (SCR) 1-2 region is selected from: (i) a structure defined by atomic coordinates of a three dimensional structure of a crystalline CR2 SCR1-2 region in complex with C3d; (ii) a structure defined by atomic coordinates selected from: (1) atomic coordinates represented in a table selected from the group consisting of Table 2 (CR2-C3d) and Table 3 (CR2 only); and, (2) atomic coordinates that define a three dimensional structure, wherein at least 50% of the structure has an average root-mean-square deviation (RMSD) from backbone atoms in secondary structure elements in at least one domain of a three dimensional structure represented by the atomic coordinates of (1) of equal to or less than about 1.0 xc3x85; and (ii) a structure defined by atomic coordinates derived from CR2 protein molecules arranged in a crystalline manner in a space group R32 so as to form a unit cell of dimensions a=b=170.5 xc3x85, c=173.8 xc3x85.
In one aspect of this embodiment, the step of identifying comprises selecting candidate compounds that potentially bind to and activate CR2.
In another aspect of this embodiment, the method further includes the step of: (c) selecting candidate compounds of (b) that inhibit the binding of CR2 to its ligand. The step (c) of selecting can include: (i) contacting the candidate compound identified in step (b) with CR2 or a fragment thereof and a CR2 ligand or a fragment thereof under conditions in which a CR2-CR2 ligand complex can form in the absence of the candidate compound; and (ii) measuring the binding affinity of the CR2 or fragment thereof to the CR2 ligand or fragment thereof; wherein a candidate inhibitor compound is selected as a compound that inhibits the binding of CR2 to its ligand when there is a decrease in the binding affinity of the CR2 or fragment thereof for the CR2 ligand or fragment thereof, as compared to in the absence of the candidate inhibitor compound. The CR2 ligand can include, but is not limited to, C3d, C3, a CR2-binding fragment of C3 containing C3d, CD23, and Epstein Barr Virus (EBV) gp350/220, or CR2-binding fragments of any of the ligands. In one aspect, the CR2 protein or fragment thereof comprises an amino acid sequence selected from the group of SEQ ID NO:4 and SEQ ID NO:6.
In another aspect of this embodiment, the method further includes the step of: (c) selecting candidate compounds that stabilizes a complex of CR2 with its ligand. Step (c) can include: (i) contacting the candidate compound identified in step (b) with a CR2-CR2 ligand complex, wherein the CR2-CR2 ligand complex comprises CR2 or a fragment thereof and a CR2 ligand, or a fragment thereof; and (ii) measuring the stability of the CR2-CR2 ligand complex of (i), wherein a candidate stabilizer compound is selected as a compound that stabilizes the CR2-CR2 ligand complex when there is an increase in the stability of the complex as compared to in the absence of the candidate stabilizer compound. In this aspect, the ligand is preferably selected from C3d, C3, a CR2-binding fragment of C3 containing C3d, CD23, and CR2-binding fragments of any of the ligands. In this aspect, the CR2 protein or fragment thereof can comprise an amino acid sequence selected from the group of SEQ ID NO:4 and SEQ ID NO:6.
In the method of identifying a compound, the step (a) of identifying can include identifying candidate compounds for binding to the SCR2 domain of the CR2. In one aspect, the step of identifying includes identifying candidate compounds for binding to the interface between the SCR1 and SCR2 domains of CR2. In another aspect, the step of identifying includes identifying candidate compounds for binding to the dimer interface between two CR2 proteins. In yet another aspect, the step of identifying includes identifying candidate compounds for binding to the interface between CR2 and C3d, C3, a CR2-binding fragment of C3 containing C3d, or a fragment thereof. In one aspect, the step of identifying includes identifying candidate compounds for binding to the B strand and the B-C loop of CR2 SCR2 comprising the segment: G79-G80-Y81-K82-I83-R84-G85-S86-T87-P88-Y89. In another aspect, the step of identifying includes identifying candidate compounds for binding to a site on the B strand of CR2 SCR2 comprising position K100. In another aspect, the step of identifying includes identifying candidate compounds for binding to a segment of CR2 SCR2 comprising V130-F131-P132-L133. In yet another aspect, the step of identifying comprises identifying candidate compounds for binding to a segment of CR2 SCR2 comprising the fragment T101-N102-F103. In one aspect of the method of identifying, the step of identifying includes identifying candidate compounds for binding to amino acid residues at positions 84 and 86 of an amino acid sequence selected from the group consisting of SEQ ID NO:4 and SEQ ID NO:6.
When the ligand is C3d, C3, or a CR2-binding fragment of C3 containing C3d, the step of identifying can include identifying candidate compounds for binding to the loop between helix 2-3 of C3d comprising the segment Q68-P69-S70-S71. In another aspect, the step of identifying can include identifying candidate compounds for binding to Helix 5 of C3d comprising the segment S104-Q105-V106-L107-C108-G109-A110-V111-K112-W113-L114-I115-L116-E117-K118-Q119-K120-P121-D122. In another aspect, the step of identifying can include identifying candidate compounds for binding to Helix 7of C3d comprising the segment N170-S171-L172-P173-G 174-S175-I176-T177-K178-A179-G180-D181-F182-L183-E184-A185.
The step of identifying a compound in the method of the present invention can include any suitable method of drug design, drug screening or identification, including, but not limited to: directed drug design, random drug design, grid-based drug design, and/or computational screening of one or more databases of chemical compounds.
Yet another embodiment of the present invention relates to a method to identify a compound that inhibits the complement receptor type 2 (CR2)-dependent infection of a host cell by Epstein Barr Virus (EBV). This method includes the steps of: (a) providing a three dimensional structure of a CR2 short consensus repeat (SCR) 1-2 region as described in detail above; (b) identifying a candidate compound for binding to the CR2 SCR 1-2 region by performing structure based drug design with the structure of (a) to identify a compound structure that binds to the three dimensional structure of the CR2 SCR 1-2 region; (c) contacting the candidate compound identified in step (b) with a cell that expresses CR2 or a ligand binding fragment thereof and an Epstein Barr Virus (EBV) particle under conditions in which the EBV particle can bind to CR2 and infect the cell in the absence of the candidate compound; and (d) measuring the intracellular EBV titer of the cell; wherein a candidate inhibitor compound is selected as a compound that inhibits the EBV titer in the cell, as compared to in the absence of the candidate inhibitor compound.
Yet another embodiment of the present invention relates to a method to identify a compound that inhibits the binding of CD23 to complement receptor type 2 (CR2). This method includes the steps of: (a) providing a three dimensional structure of a CR2 short consensus repeat (SCR) 1-2 region as described in detail above; (b) identifying a candidate compound for binding to the CR2 SCR 1-2 region by performing structure based drug design with the structure of (a) to identify a compound structure that binds to the three dimensional structure of the CR2 SCR 1-2 region; (c) contacting the candidate compound identified in step (b) with a first cell expressing CR2 or a ligand binding fragment thereof and a second cell expressing a CD23 protein or fragment thereof under conditions in which the CD23 protein or fragment thereof and the CR2 or the ligand binding fragment thereof can bind in the absence of the candidate compound; and (d) measuring a biological activity induced by the interaction of CD23 and CR2 in the first or second cell; wherein a candidate inhibitor compound is selected as a compound that inhibits the biological activity as compared to in the absence of the candidate inhibitor compound. In a preferred embodiment, the biological activity is IgE isotype switching in the first cell.
Yet another embodiment of the present invention relates to a method to identify a compound that inhibits the binding of C3d, C3 or another CR2-binding fragment of C3 containing C3d or a portion thereof, to complement receptor type 2 (CR2). This method includes the steps of: (a) providing a three dimensional structure of a CR2 short consensus repeat (SCR) 1-2 region as described in detail above; (b) identifying a candidate compound for binding to the CR2 SCR 1-2 region by performing structure based drug design with the structure of (a) to identify a compound structure that binds to the three dimensional structure of the CR2 SCR 1-2 region; (c) contacting the candidate compound identified in step (b) with a cell expressing CR2 or a fragment thereof and C3d, C3, a CR2-binding fragment of C3 containing C3d, or a fragment thereof, under conditions in which the C3d, the C3, the CR2-binding fragment of C3 containing C3d, or a fragment thereof, can bind to CR2 or the fragment thereof and enhance cell activation in the absence of the candidate compound; and (d) measuring the activation of the cell; wherein a candidate inhibitor compound is selected as a compound that inhibits cell activation, as compared to in the absence of the candidate inhibitor compound. In this embodiment, the cell in (c) can include, but is not limited to: a B cell, a T cell, a thymocyte, an epithelial cell, and a mast cell. Activation can be measured by any suitable method including, but not limited to: measurement of cytokine production by the cell, measurement of calcium mobilization in the cell, measurement of lyn tyrosine kinase activity in the cell, measurement of phosphatidylinositol 3xe2x80x2 kinase activity in the cell, measurement of activation of NF-xcexaB, measurement of activation of MAP kinases, measurement of phosphorylation of CD19 in the cell, and measurement of activation of protein kinase C (PKC) in the cell.
Another embodiment of the present invention relates to a method to inhibit complement receptor type 2 (CR2)-dependent human immunodeficiency virus-1 (HIV-1) infection of cells in a patient. This method includes the steps of administering to a patient infected with HIV-1 an inhibitor compound that inhibits the binding of C3d, C3 or another CR2-binding fragment of C3 containing C3d or a portion thereof, -opsonized HIV-1 to B cells, follicular dendritic cells, T cells or macrophages in the patient. The inhibitor compound is selected by the steps of: (a) providing a three dimensional structure of a CR2 short consensus repeat (SCR) 1-2 region as described in detail above; (b) identifying a candidate compound for binding to the CR2 SCR 1-2 region by performing structure based drug design with the structure of (a) to identify a compound structure that binds to the three dimensional structure of the CR2 SCR 1-2 region; (c) contacting the candidate compound identified in step (b) with a B cell or follicular dendritic cell expressing CR2 or a fragment thereof and C3d, C3, a CR2-binding fragment of C3 containing C3d, or a fragment thereof, under conditions in which the C3d, the C3, the CR2-binding fragment of C3 containing C3d, or the fragment thereof, can bind to CR2 and enhance B cell activation or follicular dendritic cell activation in the absence of the candidate compound; and (d) measuring the activation of the B cell or the follicular dendritic cell, wherein a candidate inhibitor compound is selected as a compound that inhibits B cell activation or follicular dendritic cell activation, as compared to in the absence of the candidate inhibitor compound.
Yet another embodiment of the present invention relates to a method to prepare a vaccine. This method includes linking a compound that increases B cell activation to an antigen to form the vaccine, wherein the compound is selected by the steps of: (a) providing a three dimensional structure of a CR2 short consensus repeat (SCR) 1-2 region as described in detail above; (b) identifying a candidate compound for binding to the CR2 SCR 1-2 region by performing structure based drug design with the structure of (a) to identify a compound structure that binds to the three dimensional structure of the CR2 SCR 1-2 region; (c) contacting the candidate compound identified in step (b) with a B cell expressing CR2 or a fragment thereof and with C3d, C3, a CR2-binding fragment of C3 containing C3d, or a fragment thereof, under conditions in which the C3d, the C3, the CR2-binding fragment of C3 containing C3d, or the fragment thereof, can bind to and activate CR2 in the absence of the candidate compound; and (d) measuring the activation of the B cell; wherein a candidate compound for use in a vaccine is selected as a compound that increases B cell activation, as compared to in the absence of the candidate compound.
Yet another embodiment of the present invention relates to a drug delivery system, which includes: (a) a drug; and, (b) a portion of a CR2 protein selected from the group of: (i) positions on strand B and the B-C loop of SCR2 including: G79-G80-Y81-K82-I83-R84-G85-S86-T87-P88-Y89; (ii) position K100 on the B strand of CR2; and, (iii) positions: V130-F131-P132-L133; and (iv) combinations of (i)-(iii). The drug is linked to the portion of CR2.
Yet another embodiment of the present invention relates to an antibody that selectively binds to CR2. The antibody binds to a portion of CR2 selected from the group of: (a) the interface between the SCR1 and SCR2 domains of CR2; (b) the dimer interface between two CR2 proteins; and, (c) the interface between CR2 and C3d. Preferably, an antibody that binds to an interface between CR2 and C3d selectively binds to a site selected from: (i) the B strand and the B-C loop of CR2 SCR2 comprising the segment: G79-G80-Y81-K82-I83-R84-G85-S86-T87-P88-Y89; (ii) the B strand of CR2 SCR2 comprising position K100; (iii) a segment of CR2 SCR2 comprising V130-F131-P132-L133; and, (iv) a segment of CR2 SCR2 comprising T101-N102-F103.
Yet another embodiment of the present invention relates to a crystal comprising complement receptor type 2 (CR2) in complex with C3d. The CR2 consists of SEQ ID NO:4, and the C3d consists of SEQ ID NO:7. The crystal effectively diffracts X-rays for the determination of the atomic coordinates of the CR2 in complex with C3d to a resolution of greater than 2.0 xc3x85, and the crystal has a space group R32 so as to form a unit cell of dimensions a=b=170.5 xc3x85, c=173.8 xc3x85.
Another embodiment of the present invention is a therapeutic composition that, when administered to an animal, enhances B cell responses in the animal. The therapeutic composition comprises a compound that stimulates the activity of a complement receptor type 2 (CR2). The compound is identified by the method that includes the steps of: (a) providing a three dimensional structure of a CR2 short consensus repeat (SCR) 1-2 region as described in detail herein; (b) identifying a candidate compound for binding to the CR2 SCR 1-2 region by performing structure based drug design with the structure of (a) to identify a compound structure that binds to the three dimensional structure of the CR2 SCR 1-2 region; (c) synthesizing the candidate compound; and (d) selecting candidate compounds that bind to and activate CR2.
Yet another embodiment relates to a therapeutic composition that, when administered to an animal, inhibits the biological activity of complement receptor type 2 (CR2) in the animal. The therapeutic composition includes a compound that inhibits the activity of a complement receptor type 2 (CR2). The compound is identified by the method that includes the steps of: (a) providing a three dimensional structure of a CR2 short consensus repeat (SCR) 1-2 region as described in detail above; (b) identifying a candidate compound for binding to the CR2 SCR 1-2 region by performing structure based drug design with the structure of (a) to identify a compound structure that binds to the three dimensional structure of the CR2 SCR 1-2 region; (c) synthesizing the candidate compound; and (d) selecting candidate compounds that inhibit the biological activity of CR2. Preferably, the compounds inhibit the formation of a complex between CR2 and a CR2 ligand. The ligand can include, C3d, C3, CR2-binding fragments of C3 containing C3d, CD23 and Epstein Barr Virus (EBV), and CR2-binding fragments any of the ligands. In one aspect, the compound inhibits the activation of CR2.
Yet another embodiment of the present invention relates to a method of preparing complement receptor type 2 (CR2) proteins having modified biological activity. This method includes the steps of: (a) providing a three dimensional structure of a CR2 short consensus repeat (SCR) 1-2 region as described in detail above; (b) analyzing the three dimensional structure to the three-dimensional structure of the CR2 SCR 1-2 region by performing structure based drug design with the structure of (a) to identify at least one site in the structure contributing to the biological activity of CR2; and (c) modifying the at least one site in a CR2 protein to alter the biological activity of the CR2 protein.
Yet another embodiment of the present invention relates to an isolated protein comprising a mutant C3d. The protein comprises an amino acid sequence that differs from SEQ ID NO:7 by an amino acid substitution selected from the group of: a non-asparagine amino acid residue at position 170, a non-isoleucine amino acid residue at position 115, and/or a non-leucine amino acid residue at position 116. The C3d mutant protein has reduced binding to complement receptor type 2 (CR2), as compared to a wild-type C3d protein. In one aspect, the mutant protein comprises an amino acid sequence selected from the group consisting of SEQ ID NO:8 and SEQ ID NO:9.